Project Number 002358T9: TROJAN IV
by Sanguinem Luna
Summary: When it's presumed Master Chief is dead, Cortana receives a lost message from Dr. Halsey containing a new project:TROJAN-IV. She does it reluctantly, ten years pass, and Master Chief is found,struggling for life. How will the SPARTAN react to the TROJANS?
1. To Clarify

I honestly want to say: Thanks for reading. Now, to clarify a few things:

12/9/11

This is about 15 years, give or take, later from the upcoming _Halo 4_

I mention, or, am going to mention, a SPARTAN named Cass. This is my character's name on _Halo: Reach_. I figured it would be easier for me than saying "Noble Six" all the time.

This is my first fanfic. Be gentle guys, I'm still not COMPLETELY caught up with the story, but I did tons of research before I wrote this. It's going to be edited often.

If anyone noticed the extra "." in the file link in Halsey's message, it was the only way to throw the whole link up there.

12/31/11

Hey guys! Sorry for the delays, Christmas was CRAZY! So, here's two new chapters!

By the way; Alex (The narrator for these two chapters) is in fact: A GIRL!

12/31/11

I want to thank everyone for the positive comments! I know I have a few errors in this chapter, please copy and paste the section in "Reviews" If you find any that I didn't, it would be an amazing help.

Now, to point out, I know my chapters are short, and in a confusing order. The first chapter starts at "John? John!" and continues, the one before that, is the prologue, and the one before that...is just the E-mail from Halsey. Not really a chapter.


	2. Messages in the Sand

**Office of Naval Intelligence****Project**** Number 002358T-9**

**Encryption Code:** Red

**Public Key:** file/ THorse/

**From:** ONI/ Dr. Catherine E. Halsey

**To:** CTN 0452-9 "Cortana"

**Subject:** TROJAN-IV

**Classification:** RESTRICTED

**In case the SPARTAN-I, SPARTAN-II were to fail, file new project directive: TROJAN-IV 002358T-9.**

**When the last SPARTAN falls, activate TROJAN-IV for full effect against the Flood contaminate. **

**Details: In closed in file **

**DOWNLOAD:**

_**ONITTP:/EPWW:TROJANHORSE/002358T-9/instruct..fbr.221.0030/IV**_

**Counting on you Cortana, to activate TROJAN-IV, even with the possibility John has fallen. **

**-Dr. Catherine Halsey**


	3. Prologue: Denials

It never even crossed my mind. The other possibilities…were endless. I sat down on the ground and rested my head to my hands. He was dead. No…I couldn't think like that. I pulled up the file on my monitor, "John-S117 Status: MIA." But…they always said that. I could pull up Lisa….Cass….MIA. I wanted to cry, I don't ever remember crying, for anything. But for this, I wanted to. I got up, and pulled up the message I had read almost twenty times:

"Counting on you Cortana, to activate TROJAN-IV, even with the possibility John has fallen."

I was undoubtedly terrified to open the file. I had gotten this message four days ago, and I already somehow wished Dr. Halsey was here to do it herself. I sighed, Lord Hood's direct order was to open it today, and follow it. I sighed, it wasn't going to open itself, and it was directed towards me. No one else was going to read it…I opened the file. My eyes widened, both in horror and surprise. There was no way….


	4. Chapter 1: John? John!

"John? John! Can you hear me? Someone come open this cryo chamber! Damn it guys…"

I groaned. The stabbing pain to my left was beginning to take its effect on me.

"John? Guys! Someone open this chamber now! That plasma damage is severe."

I tried to reach for the pain, hoping some pressure was going to help. I was stuck; I managed to wiggle, irritating the pain to my left more.

"John! Don't move! If you can hear me…just stay still! Guys! I'm not up there to do your jobs for you; I want this cryo chamber open before the sleep wears completely off!"

"Cor..." I managed to mumble. The room went quiet, she whispered a small "Damn" under her breath. I opened what I could of my eyes; the door to the chamber opened slowly, cold smoke flowing underneath my feet. I collapsed, she screamed for a stretcher, and she dropped down next to me, pulling off my helmet.

"John? Do you remember what happened?" She asked. I groaned…

"Gren…"

"Don't talk anymore. That plasma damage done to your MJOLINR armor is repairable….I can't say the same for your left waist area. It looks like you took a blow, and then a grenade got stuck, right?" She asked. I nodded slightly. She looked into my eyes, though I could barely see her, I thought I was hallucinating.

"Cortan…"

"I told you not to talk. Let's get you on the stretcher." She said softly. They pulled me on to the bed, everything in me wanted to sleep, I closed my eyes slightly…

"John! Don't you close those eyes! We're almost to the infirmary, hold on…" She yelled, the doors opened and they put me on the table. They stripped my armor off, and started applying everything they could on me.

"John…" She whispered, looking back up; her almost violet eyes were piercing me. I sighed. She flinched, and spun around. I saw a golden armor shine in the bright hospital room. My vision started to fade; I was closing my eyes…

"John!" She yelled…I grunted.

"John!" My eyes were almost shut…

"John!"


	5. Chapter 2: A Whole New World

The room was…bright. I squinted…everything was almost white. I looked at my hand, bandaged up to the shoulder. I tried to move it, the plasma burns slightly irritating it. I pulled the bandages off, reveling still peeling skin, and chars. I grunted, and got up, pulling out the I.V tube I had in my right arm. I tried walking, realizing I was stuck upright from a brace wrapped around my waist. I ripped it off, leaving the bloody bandages alone. I pulled a shirt off a rack nearby, pulling it on as I walked out of the room. The hallway seemed endless; I tried to remember what happened before I passed out. I remembered the cryo chamber…and yelling….yelling. Cortana. I sped up, hoping to make it too the door faster. She seemed unnatural; her normally blue skin was now flesh toned, and her hair was now the color of a raven. How was that possible? How long was I gone? Couldn't have been long…I swore. I shoved the door open, looking outside. The sky was golden…everything was different. I looked at the buildings…the structural design….I was on Sanghelios. Backed up…

"John! What the hell?" She yelled. I turned around, glancing at Cortana for the first time. Her raven hair had a purple glow in the light….her violet eyes glowing unnaturally against her snow like skin. I froze, was this really her? She glared at me and shook her head.

"You weren't supposed to see this yet. Any…of this."

"What…."

"Not out here. Follow me." She said coolly, pushing the door open. I walked in; she walked slowly towards the other end of the hall, opening the door to the white room. She closed the door, pulling out a key pad and entered a code, another door opening. She walked through, walking through a corridor, filled with endless amounts of people and Sangheili talking, staring. She opened a door, leading me into it.

"Sit. Running around like this must hurt those burns like hell." She said, grabbing some papers off of a table nearby. I sat down, not even noticing the throbbing burns. She sat down next to me,

"We thought you were dead John." She said, looking across the room. I looked down,

"How long?" I asked. She gazed at me, her eyes flickering,

"Ten years." I fiddled with my fingers,

"What happened…when…?"

"You were on Eridanus II. Your ship had crash landed there as far as your transmission had said. I was trying to regain contact for over 72 hours, when, Flood attacked your ship. I then realized; Eridanus II was their new breeding ground. I tried sending out everything I could, we couldn't get there fast enough. Your transmission was lost, and we couldn't explore the planet to confirm your death. And, if the Flood has somehow infected you, we wouldn't know." She said calmly. I looked at her, "And you?" "It was the last option for survival." "What do you mean?" I asked. "When you died, it was presumed the SPARTAN-II project had failed. You John, were our last hope, until, Dr. Halsey..." "Dr. Halsey?" "It's better if I show you." She said, grabbing a remote, the large screen humming to life. I looked, seeing two armored figures fighting a hologram scene. They were tall, they're armor similar to mine…the helmet almost glassed over and the colors differed. "These, are the TROJANS." 


	6. Chapter 3: The TROJANS

"Are you almost done?" He asked me. I rolled my eyes,

"Between you breathing down my back, and the plasma damage done to the system; you asking me every two minutes isn't going to make anything go faster." I snapped. He groaned,

"I'm going to go…kill something."

"Great, giving away our position to everyone. Go ahead Seth; Have fun." I said, typing on my tactical pad. He moaned again,

"This is boring. Will you hurry up?"

"Damn it Seth!" I yelled, "You come do it then! The system is fried. So, you can wait while we complete the mission or you Rambo it and answer to her. I don't care." I threw my tactical pad on the desk near me and leaned on a pillar, staring at him. I couldn't see his face, but I felt the evil glares from him peering into my soul.

"I hate you." He sighed, grabbing the pad and typing. There was banging at the door, I jumped, reaching for my energy sword. It glowed in the dimly lit room,

"You mind answering the door? Tell them I'm not home though, it's too late for company." Seth chuckled. I glared at him beneath my helmet,

"Cute. Now I'm telling you; hurry your ass up."

"My ass has nothing to do with this, but I am typing as fast as I can." He grunted. The banging got louder.

"I almost have it…"

"Your almost isn't fast enough!" I yelled, the door breaking open. I ran towards them; at first the infection form, sweeping my blade lightly as they would pop.

"Crap!" Seth grunted,

"That better be a good crap!" I yelled, stomping on an infection form that was trying to probe its way into my leg.

"Since when is crap ever good! They're getting into the system!" He screamed. I continuously threw the IFs on the ground as they tried to crawl through my armor.

"How long?" I asked

"I'm…I don't know Alex…"

"How long!" I snapped

"Fifteen minutes!" The pure and stalker forms stalked through the door, running towards me, I muttered a "shit" under my breath, and pulled the second energy sword out of the holster.

"This is going to be the longest fifteen minutes of this entire simulation."


	7. Chapter 4: The Plan

I stared at my armor; chunks of simulated Flood covered almost all the silver patches. Seth groaned sliding onto the floor,

"I'm going to feel that tomorrow."

"Feel what lazy? I killed everything." I sighed, dropping down next to him.

"Yeah…but I'm going to have some crazy Carpal Tunnel and burns later." He laughed. I chuckled, pulling my helmet off. I grabbed the pieces of dark brown hair that flew out of my pony tail, and re-tied it.

"We have to go out there."

"You can. I want to stay in here, it's warm." Seth sighed, yanking his helmet off.

"We have one more objective you big baby." I chuckled. He laughed, his big grin spreading across his face,

"Then we should go before I change my mind." He said, getting up, pulling his golden helmet back on. He reloaded his shotgun, and looked at me,

"Map us." I pulled up the map, looking at the structures around us,

"Well, you're the Leader, but, here's what I think; you see these two water towers here and here?" I asked, pointing at them on the map. He nodded, "If I can climb up one of those fast enough, kick out the ladder, and jump to the structure here; I should have a good vantage point to take out most of the Flood in the vicinity of the generator, giving you room to turn it on, and get out fast." I finished. He nodded,

"I've seen those structures though, you would have no cover, and the roofs are trashed. You willing to rely on camouflage and shields alone?" He asked.

"We don't have much of a choice. I can't get to the mountain fast enough. I'm fast…but not that fast. They'd be on my tail in a millisecond. If I stick to my plan, I at least have a shot of getting you in and out no problem."

"How many rounds do you have in the sniper rifle?" He asked. I pulled the rifle from it's holster on my back, pulling out the clip. I sighed,

"Enough."

"Doesn't…"

"We should go. I might be able to find some rounds outside." I said, throwing the rifle on my back, and pulling out one of my energy swords. I looked at the dimly lit plasma; I hadn't let this one charge long enough.

"This is going to be fun." I groaned.

"Hey, keep your head up sis. It could be worse." Seth chuckled. I cocked my head,

"Really, how?"

"There could be a tank outside." He said. I glared at him, as I pulled my silver helmet back on. We walked out the door, Seth playing with his shotgun. We stared at the battlefield. Flood was scattered everywhere. I bit my lip, and looked around; hoping to see a sniper rifle somewhere.

"Look out!" Seth yelled, pushing me out into a bale of hay, out of the sights of the giant blue plasma ball flying towards us.

"Look, there's a tank." Seth breathed. I licked the blood from biting my lip to hard, and pushed myself out of the hay.

"You suck."


	8. Chapter 5: Idiot

"You see anything Alex?"

"Yeah...trees, buildings, tons of Flood. It's such a great view. I'm thinking about buying my vacation home here." I answered. There was silence on the other end of the com. I chuckled to myself, reloading my rifle.

"Is there a path cleared yet?" Seth asked. I put my clip back in the rifle, and looked through my scope,

"You have little patches of IFs surrounding the building; I'm not wasting bullets on those. Tank forms and Stalkers are circling though; I can't get a clear shot. They know I'm up here."

"Of course they do. Half of them went down within a span of ten minutes. How about the Wraith?"

"Wraiths." I corrected. Seth paused,

"Wraiths?"

"To answer your question, yes, I have a clear shot on the gunner; the driver is keeping his head down." I responded, Seth groaned,

"Can you get a bullet in the weak spot?"

"Of course I can," I said, "But not without the possibility of giving my position away, and I wouldn't do much except damage the engine slightly at this distance." Seth let out another groan,

"I'm going to have too…."

"Yup."

"You see any…?"

"Hop on the crate to your left, then jump up to the smaller building from there. You should have a clear shot of it." I finished.

"I only have two rockets left."

"Then don't miss." I responded. He grunted as he jumped the building. Reaching for his rocket launcher, he kneeled down if front of a pillar, and glanced over at me,

"You see any clear shots for me?" He asked. I looked through my scope, and sighed,

"I can cause a diversion; taking out the gunner. There's a 50% chance of the Wraith turning around, the other fifty being it's going to aim at me. "

"I don't like those odds. But…we don't have any other options, do we?"

"Not really. Unless you want to jump it." I said. He gave a small chuckle,

"I don't like getting run over more than once in a simulation. Take the shot." He ordered. I let out a small exhale, and pulled the trigger. The pure form Flood flew off the gun, the impact of the bullet hitting his "head". The Wraith flew backwards, flipping around and launching a huge plasma ball at the cliff to its right.

"You have a shot. Go now!" I yelled over com. Seth let fired, dropping the rocket and jumping off the building; he was running for the generator.

"What the hell do you think you're doing Seth?" I snapped. His breathing got heavy as he ran for the building, shooting everything in his path. The tank exploded, almost blowing him backwards.

"I have…a clear shot. I have…to….take…it." He said, running almost out of breath. I shot a tank form that ran on his trails,

"Seth! We don't have a chance! Seth!" I yelled, throwing my rifle on my back and grabbing my energy swords. I ran off the building, landing hard on my right leg. I grunted, but managed to run towards Seth. He was ahead of me, almost to the building.

"Idiot!" I yelled, stabbing a pure form to my right. He dropped his shot gun, a swarm of IFs crawling all over his golden armor,

"Seth!" I screamed, stabbing a pure form while I ran towards my brother. He ripped a few off, trying to stomp on them, having them crawl back up his leg. He grunted, falling to his knees,

"These Sons of Bitches are heavier than…you'd think." He laughed darkly. I got to him; ripping some of the IFs and crushing them.

"You...need…to turn on the…generator." Seth breathed,

"And you?" I asked, crushing a few more IFs.

"Now would be nice Alex." He demanded. I nodded, running towards the structure holding the generator. Seth grunted loudly; I turned around to see that he was covered in swarms of IFs, and now pure forms. I paused,

"Alex! Is it…on?" Seth moaned. I started walking towards him, stabbing as much of the Flood as I could from around him.

"I'm not leaving you behind, even if you are my commander; and an idiot on at that." I snapped, Seth chuckled.

"This maybe the Flood seeping into my circuitry, but, I actually agree that I'm an idiot."

"Finally." I laughed, stabbing the last of the pure forms. Seth stood up, grabbing a IF from his arm, and stepping on it.

"Now, let's go turn on that generator."

"No need to, Beta-S402." Her loud voice booming over the speakers. The entire scene dissipated in front of us, showing only a lighted room with projectors.

"Beta and Gamma; that was fantastic. Now, I need you up at my office, ASAP. I have… someone here for you two meet." She said vaguely, as she always does.

"Great. What amazing military mind would like to see us today?" Seth grunted.

"I don't know. But, we wouldn't want to keep Mom waiting all day. You know how impatient she gets." 


End file.
